Divalent tin oxides have attracted considerable attention as novel p-type oxide semiconductors, which are essential for realizing future oxide electronic devices. Recently, p-type Sn2Nb2O7 and SnNb2O6 were developed; however, an enhanced hole mobility by reducing defect concentrations is required for practical use. In this work, we investigated the correlation between the formation of oxygen vacancy (VO), which may reduce the hole-generation efficiency and hole mobility, and the crystal structure in Sn-Nb complex oxides. Extended X-ray absorption fine structure spectroscopy and a Rietveld analysis of X-ray diffraction data revealed the preferential formation of VO at the O site bonded to the Sn ions in both the tin niobates. Moreover, a larger amount of VO around the Sn ions was found in the p-type Sn2Nb2O7 than in the p-type SnNb2O6, indicating the effect of VO on the low hole-generation efficiency. To elucidate the dependence of the formation of VO on the crystal structure, we evaluated the Sn-O bond strength based on the bond valence sum and Debye temperature. The differences in the bond strengths of the two Sn-Nb complex oxides are correlated through the steric hindrance of Sn2+ with an asymmetric electron density distribution. This suggests the importance of the material design with a focus on the local structure around the Sn ions to prevent the formation of VO in p-type Sn2+ oxides.